Job ID = 2590820 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 43,905,501 reads read : 87,811,002 reads written : 43,905,501 reads 0-length : 43,905,501 rm: cannot remove ‘[DSE]RR*’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:16:17 43905501 reads; of these: 43905501 (100.00%) were unpaired; of these: 3151584 (7.18%) aligned 0 times 30760476 (70.06%) aligned exactly 1 time 9993441 (22.76%) aligned >1 times 92.82% overall alignment rate Time searching: 00:16:18 Overall time: 00:16:18 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 20 files... [bam_rmdupse_core] 15497772 / 40753917 = 0.3803 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Mon, 12 Aug 2019 23:55:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011059/SRX5011059.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011059/SRX5011059.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011059/SRX5011059.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011059/SRX5011059.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Mon, 12 Aug 2019 23:55:56: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:55:56: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:55:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011059/SRX5011059.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011059/SRX5011059.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011059/SRX5011059.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011059/SRX5011059.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Mon, 12 Aug 2019 23:55:57: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:55:57: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:55:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011059/SRX5011059.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011059/SRX5011059.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011059/SRX5011059.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011059/SRX5011059.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Mon, 12 Aug 2019 23:55:58: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:55:58: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:56:05: 1000000 INFO @ Mon, 12 Aug 2019 23:56:06: 1000000 INFO @ Mon, 12 Aug 2019 23:56:06: 1000000 INFO @ Mon, 12 Aug 2019 23:56:13: 2000000 INFO @ Mon, 12 Aug 2019 23:56:15: 2000000 INFO @ Mon, 12 Aug 2019 23:56:15: 2000000 INFO @ Mon, 12 Aug 2019 23:56:22: 3000000 INFO @ Mon, 12 Aug 2019 23:56:24: 3000000 INFO @ Mon, 12 Aug 2019 23:56:24: 3000000 INFO @ Mon, 12 Aug 2019 23:56:30: 4000000 INFO @ Mon, 12 Aug 2019 23:56:32: 4000000 INFO @ Mon, 12 Aug 2019 23:56:32: 4000000 INFO @ Mon, 12 Aug 2019 23:56:39: 5000000 INFO @ Mon, 12 Aug 2019 23:56:40: 5000000 INFO @ Mon, 12 Aug 2019 23:56:41: 5000000 INFO @ Mon, 12 Aug 2019 23:56:48: 6000000 INFO @ Mon, 12 Aug 2019 23:56:49: 6000000 INFO @ Mon, 12 Aug 2019 23:56:50: 6000000 INFO @ Mon, 12 Aug 2019 23:56:57: 7000000 INFO @ Mon, 12 Aug 2019 23:56:58: 7000000 INFO @ Mon, 12 Aug 2019 23:56:59: 7000000 INFO @ Mon, 12 Aug 2019 23:57:06: 8000000 INFO @ Mon, 12 Aug 2019 23:57:08: 8000000 INFO @ Mon, 12 Aug 2019 23:57:08: 8000000 INFO @ Mon, 12 Aug 2019 23:57:14: 9000000 INFO @ Mon, 12 Aug 2019 23:57:17: 9000000 INFO @ Mon, 12 Aug 2019 23:57:17: 9000000 INFO @ Mon, 12 Aug 2019 23:57:24: 10000000 INFO @ Mon, 12 Aug 2019 23:57:26: 10000000 INFO @ Mon, 12 Aug 2019 23:57:27: 10000000 INFO @ Mon, 12 Aug 2019 23:57:33: 11000000 INFO @ Mon, 12 Aug 2019 23:57:33: 11000000 INFO @ Mon, 12 Aug 2019 23:57:37: 11000000 INFO @ Mon, 12 Aug 2019 23:57:40: 12000000 INFO @ Mon, 12 Aug 2019 23:57:43: 12000000 INFO @ Mon, 12 Aug 2019 23:57:47: 12000000 INFO @ Mon, 12 Aug 2019 23:57:47: 13000000 INFO @ Mon, 12 Aug 2019 23:57:52: 13000000 INFO @ Mon, 12 Aug 2019 23:57:54: 14000000 INFO @ Mon, 12 Aug 2019 23:57:56: 13000000 INFO @ Mon, 12 Aug 2019 23:58:01: 14000000 INFO @ Mon, 12 Aug 2019 23:58:02: 15000000 INFO @ Mon, 12 Aug 2019 23:58:06: 14000000 INFO @ Mon, 12 Aug 2019 23:58:09: 16000000 INFO @ Mon, 12 Aug 2019 23:58:11: 15000000 INFO @ Mon, 12 Aug 2019 23:58:16: 17000000 INFO @ Mon, 12 Aug 2019 23:58:16: 15000000 INFO @ Mon, 12 Aug 2019 23:58:20: 16000000 INFO @ Mon, 12 Aug 2019 23:58:23: 18000000 INFO @ Mon, 12 Aug 2019 23:58:26: 16000000 INFO @ Mon, 12 Aug 2019 23:58:29: 17000000 INFO @ Mon, 12 Aug 2019 23:58:30: 19000000 INFO @ Mon, 12 Aug 2019 23:58:35: 17000000 INFO @ Mon, 12 Aug 2019 23:58:37: 20000000 INFO @ Mon, 12 Aug 2019 23:58:39: 18000000 INFO @ Mon, 12 Aug 2019 23:58:44: 21000000 INFO @ Mon, 12 Aug 2019 23:58:45: 18000000 INFO @ Mon, 12 Aug 2019 23:58:48: 19000000 INFO @ Mon, 12 Aug 2019 23:58:51: 22000000 INFO @ Mon, 12 Aug 2019 23:58:55: 19000000 INFO @ Mon, 12 Aug 2019 23:58:57: 20000000 INFO @ Mon, 12 Aug 2019 23:58:59: 23000000 INFO @ Mon, 12 Aug 2019 23:59:04: 20000000 INFO @ Mon, 12 Aug 2019 23:59:06: 24000000 INFO @ Mon, 12 Aug 2019 23:59:07: 21000000 INFO @ Mon, 12 Aug 2019 23:59:13: 25000000 INFO @ Mon, 12 Aug 2019 23:59:14: 21000000 INFO @ Mon, 12 Aug 2019 23:59:15: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:59:15: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:59:15: #1 total tags in treatment: 25256145 INFO @ Mon, 12 Aug 2019 23:59:15: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:59:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 23:59:15: #1 tags after filtering in treatment: 25256145 INFO @ Mon, 12 Aug 2019 23:59:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:59:15: #1 finished! INFO @ Mon, 12 Aug 2019 23:59:15: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:59:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:59:16: 22000000 INFO @ Mon, 12 Aug 2019 23:59:17: #2 number of paired peaks: 213 WARNING @ Mon, 12 Aug 2019 23:59:17: Fewer paired peaks (213) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 213 pairs to build model! INFO @ Mon, 12 Aug 2019 23:59:17: start model_add_line... INFO @ Mon, 12 Aug 2019 23:59:18: start X-correlation... INFO @ Mon, 12 Aug 2019 23:59:18: end of X-cor INFO @ Mon, 12 Aug 2019 23:59:18: #2 finished! INFO @ Mon, 12 Aug 2019 23:59:18: #2 predicted fragment length is 66 bps INFO @ Mon, 12 Aug 2019 23:59:18: #2 alternative fragment length(s) may be 4,66 bps INFO @ Mon, 12 Aug 2019 23:59:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011059/SRX5011059.10_model.r WARNING @ Mon, 12 Aug 2019 23:59:18: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:59:18: #2 You may need to consider one of the other alternative d(s): 4,66 WARNING @ Mon, 12 Aug 2019 23:59:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 23:59:18: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:59:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:59:24: 22000000 INFO @ Mon, 12 Aug 2019 23:59:25: 23000000 INFO @ Mon, 12 Aug 2019 23:59:34: 23000000 INFO @ Mon, 12 Aug 2019 23:59:35: 24000000 INFO @ Mon, 12 Aug 2019 23:59:43: 24000000 INFO @ Mon, 12 Aug 2019 23:59:44: 25000000 INFO @ Mon, 12 Aug 2019 23:59:46: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:59:46: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:59:46: #1 total tags in treatment: 25256145 INFO @ Mon, 12 Aug 2019 23:59:46: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:59:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 23:59:47: #1 tags after filtering in treatment: 25256145 INFO @ Mon, 12 Aug 2019 23:59:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:59:47: #1 finished! INFO @ Mon, 12 Aug 2019 23:59:47: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:59:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:59:49: #2 number of paired peaks: 213 WARNING @ Mon, 12 Aug 2019 23:59:49: Fewer paired peaks (213) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 213 pairs to build model! INFO @ Mon, 12 Aug 2019 23:59:49: start model_add_line... INFO @ Mon, 12 Aug 2019 23:59:49: start X-correlation... INFO @ Mon, 12 Aug 2019 23:59:49: end of X-cor INFO @ Mon, 12 Aug 2019 23:59:49: #2 finished! INFO @ Mon, 12 Aug 2019 23:59:49: #2 predicted fragment length is 66 bps INFO @ Mon, 12 Aug 2019 23:59:49: #2 alternative fragment length(s) may be 4,66 bps INFO @ Mon, 12 Aug 2019 23:59:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011059/SRX5011059.05_model.r WARNING @ Mon, 12 Aug 2019 23:59:49: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:59:49: #2 You may need to consider one of the other alternative d(s): 4,66 WARNING @ Mon, 12 Aug 2019 23:59:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 23:59:49: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:59:49: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:59:53: 25000000 INFO @ Mon, 12 Aug 2019 23:59:55: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:59:55: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:59:55: #1 total tags in treatment: 25256145 INFO @ Mon, 12 Aug 2019 23:59:55: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:59:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 23:59:56: #1 tags after filtering in treatment: 25256145 INFO @ Mon, 12 Aug 2019 23:59:56: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:59:56: #1 finished! INFO @ Mon, 12 Aug 2019 23:59:56: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:59:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:59:58: #2 number of paired peaks: 213 WARNING @ Mon, 12 Aug 2019 23:59:58: Fewer paired peaks (213) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 213 pairs to build model! INFO @ Mon, 12 Aug 2019 23:59:58: start model_add_line... INFO @ Mon, 12 Aug 2019 23:59:58: start X-correlation... INFO @ Mon, 12 Aug 2019 23:59:58: end of X-cor INFO @ Mon, 12 Aug 2019 23:59:58: #2 finished! INFO @ Mon, 12 Aug 2019 23:59:58: #2 predicted fragment length is 66 bps INFO @ Mon, 12 Aug 2019 23:59:58: #2 alternative fragment length(s) may be 4,66 bps INFO @ Mon, 12 Aug 2019 23:59:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011059/SRX5011059.20_model.r WARNING @ Mon, 12 Aug 2019 23:59:58: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:59:58: #2 You may need to consider one of the other alternative d(s): 4,66 WARNING @ Mon, 12 Aug 2019 23:59:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 23:59:58: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:59:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:00:17: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:00:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011059/SRX5011059.10_peaks.xls INFO @ Tue, 13 Aug 2019 00:00:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011059/SRX5011059.10_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:00:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011059/SRX5011059.10_summits.bed INFO @ Tue, 13 Aug 2019 00:00:46: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (3539 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 00:00:49: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:00:58: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:01:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011059/SRX5011059.05_peaks.xls INFO @ Tue, 13 Aug 2019 00:01:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011059/SRX5011059.05_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:01:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011059/SRX5011059.05_summits.bed INFO @ Tue, 13 Aug 2019 00:01:18: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (7144 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 00:01:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011059/SRX5011059.20_peaks.xls INFO @ Tue, 13 Aug 2019 00:01:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011059/SRX5011059.20_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:01:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011059/SRX5011059.20_summits.bed INFO @ Tue, 13 Aug 2019 00:01:28: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1540 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。